Mutations in the cardiac beta-myosin heavy chain (MHC) gene of 50 Japanese patients with hypertrophic cardiomyopathy (HCM) were investigated by polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) analysis. A novel deletion mutation was detected in exon 3 of the cardiac beta-MHC gene in a Japanese family with HCM. Sequencing analysis revealed a three nucleotide deletion at codon 10 leading to a deletion of a glycine residue, which has been conserved in the myosin gene from birds to humans. Because this deletion mutation was not detected in other healthy family members, it was suggested that this 10Gly deletion is the cause of HCM in this family. The same deletion mutation has been found in three other unrelated patients with HCM. This is the first report of a one codon deletion in the beta-MHC gene in patients with HCM.